Castanet: a pipeline for rapid analysis of targeted multi-pathogen genomic data.

ABSTRACT:

Motivation

Target enrichment strategies generate genomic data from multiple pathogens in a single process, greatly improving sensitivity over metagenomic sequencing and enabling cost-effective, high-throughput surveillance and clinical applications. However, uptake by research and clinical laboratories is constrained by an absence of computational tools that are specifically designed for the analysis of multi-pathogen enrichment sequence data. Here we present an analysis pipeline, Castanet, for use with multi-pathogen enrichment sequencing data. Castanet is designed to work with short-read data produced by existing targeted enrichment strategies, but can be readily deployed on any BAM file generated by another methodology. Also included are an optional graphical interface and insta

SUBMITTER: Mayne R 

PROVIDER: S-EPMC11494375 | biostudies-literature | 2024 Oct

REPOSITORIES: biostudies-literature